Method of isolating nucleic acid from specimens in liquid-based cytology preservatives containing formaldehyde

ABSTRACT

Method, composition, kit and system for isolating amplifiable nucleic acid from specimens preserved in a liquid-based cytology preservative that contains formaldehyde. The technique relies on the use of 2-imidazolidone and a protease enzyme, such as proteinase K, at elevated temperatures. Advantageously, RNA can be isolated and used as a template in nucleic acid amplification reactions.

CROSS-REFERENCE TO RELATED APPLICATION

The present application is a non-provisional of 61/946,637 filed Feb.28, 2014, which is incorporated by reference in its entirety for allpurposes.

FIELD OF THE INVENTION

The present invention relates to the field of biotechnology. Moreparticularly, the invention relates to methods of isolating nucleic acidfrom samples fixed in a formaldehyde-containing liquid-based cytologypreservative, where isolated RNA is suitable for use as a template innucleic acid amplification procedures.

BACKGROUND OF THE INVENTION

Laboratory personnel engaged in molecular analysis of nucleic acidisolated from formaldehyde-fixed samples appreciate that certainrestrictions apply to the use of this sample type. This is becauseformaldehyde, and certain other chemical fixatives, chemically modifyproteins and nucleic acids. These modifications are known to compromisethe utility of nucleic acid in subsequent analyses.

Particular difficulties result from the well-known chemical modificationof DNA, RNA and proteins. Indeed, Masuda et al., (Nucleic Acids Res.,27:4436-4443 (1999)) investigated the reason formalin-fixed samples arepoor materials for molecular biological applications. The authorsdemonstrated that, while treatment with proteinase K solubilized fixedtissues and enabled RNA extraction, the extracted RNA was of onlylimited use as a PCR template. Further investigation revealed chemicaladdition of mono-methylol groups (—CH₂OH) to all four bases, as well asevidence for adenine dimerization through methylene bridging. Certainmodifications could be reversed by elevating the temperature informalin-free buffer. However, the instability of RNA can make the useof high temperature conditions undesirable.

Earlier approaches for treating formaldehyde-fixed samples have met withsome success. For example, Khripin et al., in published U.S. PatentApplication 2011/0196146 A1 described the use of hydrazine- andhydrazide-containing formaldehyde-scavenging compounds during isolationof nucleic acids from cellular material disposed in a liquid-basedcytology preservative containing formaldehyde (e.g., semicarbazide;thiosemicarbazide; carbazide; thiocarbazide; N-aminoguanidine and a saltthereof, including hydrochloride salts; N,N-diaminoguanidine and a saltthereof, including dihydrochloride salts; acetylhydrazide; adipic aciddihydrazide; succinic acid dihydrazide; formic hydrazide; maleic aciddihydrazide; malonic acid dihydrazide; benzenesulfonylhydrazide;tosylhydrazide; methylsulfonylhydrazide). Rather than employing nucleicacid amplification as a measure of nucleic acid integrity, the inventorsemployed a hybrid capture protocol wherein a cocktail of RNA probeshybridized to isolated nucleic acid. This was followed by antibodybinding to the RNA:DNA hybrids, and a subsequent signal amplificationprocedure to determine the presence of DNA target nucleic acids. Indeed,Khripin et al., refer to U.S. Pat. No. 6,228,578 for instructing nucleicacid detection, where that reference describes treatment of nucleic acidsamples under conditions of strong alkali and hightemperature—conditions known to hydrolyze RNA. Thus, Khripin et al., donot address rendering nucleic acids suitable for use as templates innucleic acid amplification reactions, nor present sufficient disclosureto allow detection of RNA targets from formaldehyde-fixed specimens.

The techniques disclosed herein address the need for rapid and efficientisolation of intact nucleic acid, such as RNA, from specimens preservedin formaldehyde-containing liquid-based cytology preservatives.

SUMMARY OF THE CLAIMED INVENTION

In one aspect, the invention relates to a method of processing aspecimen that includes a clinical sample disposed in a liquid-basedcytology preservative that contains formaldehyde. The method begins withthe step of combining the specimen with a protease enzyme and2-imidazolidone or other formaldehyde scavenger to create a reactionmixture. This is followed by incubating the reaction mixture at anelevated temperature for a period of time sufficient to reverse chemicalmodifications by formaldehyde of nucleic acid that may be contained inthe specimen. By this step, at least some of the chemical modificationscaused by reaction between formaldehyde and either nucleic acids orproteins are reversed. For example, chemical crosslinks may be broken.Next there is a step for isolating a nucleic acid from the reactionmixture after the incubating step. Finally, there is a step forperforming an in vitro amplification reaction using the nucleic acidfrom the isolating step as templates.

In some methods, the reversing releases nucleic acids in the specimenfrom formaldehyde-induced crosslinking to polypeptides in the specimen.In some methods, the protease frees the nucleic acids from theformaldehyde-induced crosslinking and 2-imidazolidone inhibits inductionof new cross-links between nucleic acids and polypeptides in the sample.

In some methods, the sample has been disposed in the liquid-basedcytology preservative for 7-120 days before performing step (a).

In some methods, the incubating step is for no more than 30 minutes orthe incubating step is between about 5 minutes and 30 minutes or theincubating step is for no more than 15 min.

In some methods, the yield of amplified nucleic acid after step (d) ishigher than in control amplifications omitting either the proteinase or2-imidazolidone. In some methods, the yield of amplified nucleic acidafter step (d) is at least 10% higher than either of controlamplifications omitting either proteinase or 2-imidazolidone. In somemethods, at least 90% of the nucleic acid molecules in the sample arefree of the cross-links after the incubating step.

In some methods, final concentration of 2-imidazolidone before theincubation step is 1 to 5 or 2-5 fold by moles greater than finalmaximum concentration of the formaldehyde. In some methods, theproteinase is proteinase-K present at a concentration of 4.3 to 43 U/ml.In some methods, the temperature of the incubating step is about 60-100°C. In some methods, the temperature of the incubating step is 85-95° C.In some methods, the temperature of the incubating step is 91-95° C. Insome methods, the temperature of the incubating step is 90° C.

In some methods, the proteinase and formaldehyde scavenger are combinedsimultaneously with the specimen. In some methods, the proteinase iscombined with the specimen before formaldehyde scavenger. In somemethods, the formaldehyde scavenger is combined with the specimen beforethe proteinase.

In some methods, the amplification is a transcription mediatedamplification, single-primer nucleic acid amplification, nucleic acidsequence-based amplification, polymerase chain Reaction, stranddisplacement amplification, self-sustained sequence replication or DNAligase chain reaction. In some methods, the nucleic acids comprise DNAand in some methods RNA. In some methods, the isolated nucleic acid isDNA and in some methods RNA.

In some methods, the nucleic acid is isolated by a capture assay with acapture probe hybridizing to the nucleic acid to be isolated and to animmobilized probe. In some methods, the immobilized probe is immobilizedto a magnetic bead.

In some methods, the assay positivity of amplified nucleic acid ishigher than assay positivity of amplified nucleic acids obtained fromreaction mixture omitting either proteinase or the formaldehydescavenger. In some methods, the assay positivity of amplified nucleicacid is at least about 12% higher than assay positivity of amplifiednucleic acids obtained from reaction mixture omitting either proteinaseor 2-imidazolidone. In some methods, the assay positivity of amplifiednucleic acid after step (d) is about 95% after 21 days.

In some methods, the isolated nucleic acid is human papillomavirus (HPV)RNA target nucleic acid. In some methods, the specimen is a cervicalcell specimen.

In another aspect, the invention relates to a composition of matter thatincludes the following components: 2-imidazolidone; proteinase K; EDTA;and a pH buffer.

In another aspect, the invention relates to a kit for processing aspecimen preserved in a liquid-based cytology preservative that containsformaldehyde. The kit includes a first vial containing a lyophilizedproteinase K enzyme. As well, the kit includes a second vial containinga reconstitution buffer for reconstituting the lyophilized proteinase Kenzyme. This reconstitution buffer includes an amount of a pH buffer, anamount of EDTA, and an amount of 2-imidazolidone.

In another aspect, the invention relates to a system for processingnucleic acid-containing samples preserved in a liquid-based cytologypreservative that contains formaldehyde. The system components include:a programmable controller; a pipetting device in communication with theprogrammable controller; a first holder for a reaction vial; and asecond holder for a reagent vial. In accordance with this aspect of theinvention, the programmable controller is configured by softwareinstructions to cause the pipetting device to transfer an aliquot ofliquid from the reagent vial to the reaction vial when the reagent vialcontains a solution comprising 2-imidazolidone, proteinase K, EDTA, anda pH buffer. As well as these components, the reaction vial can containa specimen preserved in formaldehyde as further described belowintroduced before or after the other components. The same or otherpipetting device can be used for introducing the specimen into thereaction vial, optionally with the programmable controller beingconfigured by software to cause such pipetting device to operate. Thesystem can also include a heater for heating the reaction vial and itscontents for a controlled period of time, optionally subject to thecontrol of the programmable controller configure by suitable software.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a bar graph showing % positivity in the HPV RNA amplificationand detection assay performed using in vitro transcripts. Threeconditions used in the procedure were: (1) specimens preserved inTHINPREP liquid-based cytology preservative (solid fill); (2) specimenspreserved in SUREPATH liquid-based cytology preservative and treatedwith proteinase K enzyme (diagonal fill); and (3) specimens preserved inSUREPATH liquid-based cytology preservative and treated with thecombination of 2-imidazolidone and proteinase K enzyme at elevatedtemperature (open bars).

FIGS. 2A-2C are bar graphs showing % positivity in the HPV RNAamplification and detection assay performed using human cell linescontaining different HPV types. FIG. 2A shows results obtained usingSiHa cells that contained HPV 16. FIG. 2B shows results obtained usingHeLa cells that contained HPV 18. FIG. 2C shows results obtained usingMS751 cells that contained HPV 45. In each of FIGS. 2A-2C, open barsindicate % positivity (left scale), and thick horizontal lines indicateaverage signal/cutoff ratio (right scale).

FIGS. 3A-3B are line graphs showing % positive reactions (vertical axis)as a function of time (days stored in liquid-based cytology preservativecontaining formaldehyde). Both graphs present results from procedurescarried out using 30 cells/reaction. FIG. 3A presents results obtainedusing SiHa cells. FIG. 3B presents results obtained using HeLa cells.The different lines indicate treatment with proteinase K alone (▪); andwith the combination of 2-imidazolidone and proteinase K (♦).

FIG. 4 is a line graph showing % positivity as a function of storagetime at 2-8° C. The lines represent results for a clinical specimendiluted 1:10 (♦), and diluted 1:100 (▪).

FIG. 5 is a diagram depicting key elements of an exemplary workflow.

FIG. 6 shows a possible reaction mechanism of formaldehyde, proteinase Kand 2-imidazolidone.

DEFINITIONS

Unless otherwise described, scientific and technical terms used hereinhave the same meaning as commonly understood by those skilled in the artof molecular biology based on technical literature, e.g., Dictionary ofMicrobiology and Molecular Biology, 2nd ed. (Singleton et al., 1994,John Wiley & Sons, New York, N.Y.), or other well-known technicalpublications related to molecular biology. Unless otherwise described,techniques employed or contemplated herein are standard methods wellknown in the art of molecular biology.

All patents, applications, published applications and other publicationsreferred to herein are incorporated by reference in their entireties. Ifa definition set forth in this section is contrary to or otherwiseinconsistent with a definition set forth in the patents, applications,published applications and other publications that are hereinincorporated by reference, the definition set forth in this sectionprevails over the definition that is incorporated herein by reference.

As used herein, “a” or “an” means “at least one” or “one or more.”

Approximating language, as used herein throughout the specification andclaims, may be applied to modify any quantitative or qualitativerepresentation that could permissibly vary without resulting in a changein the basic function to which it is related. Accordingly, a valuemodified by a term such as “about” or “approximately” is not to belimited to the precise value specified, and may include values thatdiffer from the specified value.

For clarification, “formaldehyde,” in its basic form (CH₂O), is a gas.The liquid called “formalin” is actually a mixture of formaldehyde gasand water. However, as used herein, “formaldehyde” can refer to themolecule (CH₂O) that is dissolved in an aqueous solution.

As used herein, “liquid-based cytology” refers to liquid-basedgynecologic specimen collection, wherein a sample for cervicovaginaltesting collected in the conventional manner with one of the brushinstruments but, instead of being spread onto a glass slide, it istransferred to a vial of liquid preservative or “fixative.” Thepreserved specimen can be used for microscopy or molecular analysis.

As used herein, a “specimen” is something collected as an example of aparticular kind of thing. Biological specimens include any tissue ormaterial derived from a living or dead organism that may contain ananalyte, such as a nucleic acid analyte. Preferred biological specimensinclude respiratory tissue, exudates (e.g., bronchoalveolar lavage),biopsy, sputum, peripheral blood, plasma, serum, lymph node,gastrointestinal tissue, feces, urine, or other fluids, tissues ormaterials. Highly preferred biological specimens include cells collectedfrom the outer opening of the cervix, as may be obtained in connectionwith PAP testing.

As used herein, the term “sample” refers to a portion or quantity ofmaterial for use in testing, where that portion can be informative aboutthe thing from which it was taken. Samples may be from any source, suchas biological specimens or environmental sources.

As used herein, the term “nucleic acid” refers to a polynucleotidecompound, which includes oligonucleotides, comprising nucleosides ornucleoside analogs that have nitrogenous heterocyclic bases or baseanalogs, covalently linked by standard phosphodiester bonds or otherlinkages. Nucleic acids include RNA, DNA, chimeric DNA-RNA polymers oranalogs thereof.

By “analyte nucleic acid” is meant a polynucleotide of interest that isto be detected or quantified. The genome of a particular virus wouldexemplify an analyte nucleic acid.

As used herein, a “test sample” is any sample to be investigated for thepresence of a particular analyte nucleic acid.

As used herein, “elevated” temperature conditions refer to a temperaturehigher than room temperature. Preferably, elevated temperatures are inthe range of from 60° C.-100° C., more preferably in the range of from65° C.-95° C., sometimes in the range of from 80° C.-90° C., sometimes81-98° C., 85-98° C., 85-95° C., 90-95° C., 91-95° C. or 91-99° C., andsometimes about 90° C. Use of temperatures above 80° C., e.g., 85-98°C., 90° C., or 91-95° C. can result in increased assay sensitivity asfurther defined below, which is surprising because proteinase K undergoincreasing denaturation as the temperature is increased over 65° C., andwould not normally be recommended for use at temperatures above 85° C.or 90° C. because of excessive denaturation. Although practice of theinvention is not dependent on discerning the mechanism for thisunexpected benefit from higher temperatures, this result may indicatethat promotion of 2-imidazolidone scavenging of formaldehyde at theelevated temperature more than compensates for some reduction inproteinase K activity. Preferably, in all of these instances, reactionmixtures including a clinical sample in liquid-based cytologypreservative, 2-imidazolidone, protease, EDTA and pH buffer are exposedto elevated temperatures for a period of time from 10 minutes to 30minutes, and preferably from 10 minutes to not more than 20 minutes, andsometimes for up to 15 minutes or about 15 minutes.

An “amplicon” is a polynucleotide product of an in vitro nucleic acidamplification reaction, wherein a target nucleic acid sequence served asthe template for synthesis of copies or amplification products.

By “target” or “target nucleic acid” is meant a nucleic acid containinga sequence that is to be amplified, detected and/or quantified. A targetnucleic acid sequence that is to be amplified preferably are positionedbetween two oppositely disposed oligonucleotides, and includes theportion of the target nucleic acid that is complementary to each of theoligonucleotides.

By “amplification” or “nucleic acid amplification” or “in vitro nucleicacid amplification” and the like is meant any known procedure forobtaining multiple copies, allowing for RNA and DNA equivalents, of atarget nucleic acid sequence or its complement or fragments thereof.

To aid in understanding of some of the embodiments disclosed herein, theTMA method that has been described in detail previously (e.g., U.S. Pat.Nos. 5,399,491, 5,554,516 and 5,824,518) is briefly summarized. In TMA,a target nucleic acid that contains the sequence to be amplified isprovided as single stranded nucleic acid (e.g., ssRNA or ssDNA). Anyconventional method of converting a double stranded nucleic acid (e.g.,dsDNA) to a single-stranded nucleic acid may be used. A promoter primerbinds specifically to the target nucleic acid at its target sequence anda reverse transcriptase (RT) extends the 3′ end of the promoter primerusing the target strand as a template to create a cDNA copy, resultingin a RNA:cDNA duplex. RNase activity (e.g., RNase H of RT enzyme)digests the RNA of the RNA:cDNA duplex and a second primer bindsspecifically to its target sequence in the cDNA, downstream from thepromoter-primer end. Then RT synthesizes a new DNA strand by extendingthe 3′ end of the second primer using the cDNA as a template to create adsDNA that contains a functional promoter sequence. RNA polymerasespecific for the functional promoter initiates transcription to produceabout 100 to 1000 RNA transcripts (amplified copies or amplicons)complementary to the initial target strand. The second primer bindsspecifically to its target sequence in each amplicon and RT creates acDNA from the amplicon RNA template to produce a RNA:cDNA duplex. RNasedigests the amplicon RNA from the RNA:cDNA duplex and thetarget-specific sequence of the promoter primer binds to itscomplementary sequence in the newly synthesized DNA and RT extends the3′ end of the promoter primer as well as the 3′ end of the cDNA tocreate a dsDNA that contains a functional promoter to which the RNApolymerase binds and transcribes additional amplicons that arecomplementary to the target strand. Autocatalytic cycles that use thesesteps repeatedly during the reaction produce about a billion-foldamplification of the initial target sequence. Amplicons may be detectedduring amplification (real-time detection) or at an end point of thereaction (end-point detection) by using a probe that binds specificallyto a sequence contained in the amplicons. Detection of a signalresulting from the bound probes indicates the presence of the targetnucleic acid in the sample.

As used herein, “detection” of the amplified products may beaccomplished by using any known method. For example, the amplifiednucleic acids may be associated with a surface that results in adetectable physical change (e.g., an electrical change). Amplifiednucleic acids may be detected in solution phase or by concentrating themin or on a matrix and detecting labels associated with them (e.g., anintercalating agent such as ethidium bromide). Other detection methodsuse probes complementary to a sequence in the amplified product anddetect the presence of the probe:product complex, or use a complex ofprobes to amplify the signal detected from amplified products (e.g.,U.S. Pat. Nos. 5,424,413, 5,451,503 and 5,849,481). Other detectionmethods use a probe in which signal production is linked to the presenceof the target sequence because a change in signal results only when thelabeled probe binds to amplified product, such as in a molecular beacon,molecular torch, or hybridization switch probe (e.g., U.S. Pat. Nos.5,118,801, 5,312,728, 5,925,517, 6,150,097, 6,361,945, 6,534,274,6,835,542, 6,849,412 and 8,034,554; and U.S. Pub. No. 2006/0194240 A1).Such probes typically use a label (e.g., fluorophore) attached to oneend of the probe and an interacting compound (e.g., quencher) attachedto another location of the probe to inhibit signal production from thelabel when the probe is in one conformation (“closed”) that indicates itis not hybridized to amplified product, but a detectable signal isproduced when the probe is hybridized to the amplified product whichchanges its conformation (to “open”). Detection of a signal fromdirectly or indirectly labeled probes that specifically associate withthe amplified product indicates the presence of the target nucleic acidthat was amplified.

As used herein, a “probe” is an oligonucleotide that hybridizesspecifically to a target sequence in a nucleic acid, preferably in anamplified nucleic acid, under conditions that promote hybridization, toform a detectable hybrid.

As used herein, the term “contacting” means bringing two or morecomponents together. Contacting can be achieved by mixing all thecomponents in a fluid or semi-fluid mixture. Contacting can also beachieved when one or more components are brought into physical contactwith one or more other components on a solid surface such as a solidtissue section or a substrate.

As used herein, the term “target capture” refers to selectivelyseparating a target nucleic acid from other components of a samplemixture, such as cellular fragments, organelles, proteins, lipids,carbohydrates, or other nucleic acids. A target capture system may bespecific and selectively separate a predetermined target nucleic acidfrom other sample components (e.g., by using a nucleic acid sequencespecific to the intended target nucleic acid), or it may be nonspecificand selectively separate a target nucleic acid from other samplecomponents by using other characteristics of the target (e.g., aphysical trait of the target nucleic acid that distinguishes it fromother sample components which do not exhibit that physicalcharacteristic, such as hybridization to a non-specific nucleic acid,binding to a porous glass bead, capture and elution in a silica packedcolumn). Preferred nucleic acid hybridization target capture methods andcompositions have been previously described in detail (U.S. Pat. Nos.5,750,338, 6,060,246, 6,110,678, 6,534,273 and 7,993,853; and US Pub.No. 2008/0286775 A1). Preferred target capture embodiments use a targetcapture oligonucleotide in solution phase and an immobilized captureprobe attached to a support to form a complex with the target nucleicacid and separate the captured target from other components.

As used herein, the term “target capture oligonucleotide” refers to atleast one nucleic acid oligonucleotide that bridges or joins a targetnucleic acid and an immobilized capture probe by using binding pairmembers, such as complementary nucleic acid sequences or biotin andstreptavidin. In one approach, the target capture oligonucleotide bindsnonspecifically to the target nucleic acid and immobilizes it to a solidsupport. In a different approach, a target specific (TS) sequence of thetarget capture oligonucleotide binds specifically to a sequence in thetarget nucleic acid. In both approaches the target captureoligonucleotide includes an immobilized capture probe-binding regionthat binds to an immobilized capture probe (e.g., by specific bindingpair interaction). In embodiments in which the TS sequence and theimmobilized capture probe-binding region are both nucleic acidsequences, they may be covalently joined to each other, or may be ondifferent oligonucleotides joined by one or more linkers.

An “immobilized capture probe” provides a means for joining a targetcapture oligonucleotide to a solid support. The immobilized captureprobe is a base sequence recognition molecule joined to the solidsupport, which facilitates separation of bound target polynucleotidefrom unbound material. Any known solid support may be used, such asmatrices and particles free in solution. For example, solid supports maybe nitrocellulose, nylon, glass, polyacrylate, mixed polymers,polystyrene, silane polypropylene and, preferably, magneticallyattractable particles. Particularly preferred supports include magneticspheres that are monodisperse (i.e., uniform in size ± about 5%),thereby providing consistent results, which is particularly advantageousfor use in an automated assay. The immobilized capture probe may bejoined directly (e.g., via a covalent linkage or ionic interaction), orindirectly to the solid support. Common examples of useful solidsupports include magnetic particles or beads.

As used herein, the term “separating” or “purifying” generally refers toremoval of one or more components of a mixture, such as a sample, fromone or more other components in the mixture. Sample components includenucleic acids in a generally aqueous solution phase, which may includecellular fragments, proteins, carbohydrates, lipids, and othercompounds. Preferred embodiments separate or remove at least 70% to 80%,and more preferably about 95%, of the target nucleic acid from othercomponents in the mixture.

By “kit” is meant a packaged combination of materials, typicallyintended for use in conjunction with each other. Kits in accordance withthe invention may include instructions or other information in a“tangible” form (e.g., printed information, electronically recorded on acomputer-readable medium, or otherwise recorded on a machine-readablemedium such as a bar code for storing numerical values).

By “consisting essentially of” is meant that additional component(s),composition(s) or method step(s) that do not materially change the basicand novel characteristics of the present invention may be included inthe present invention. Any component(s), composition(s), or methodstep(s) that have a material effect on the basic and novelcharacteristics of the present invention would fall outside of thisterm.

Unless otherwise apparent from the context, “about” indicates variationsimplicit in the accuracy with which a value can be measured.

“Reversing” modifications of DNA refers to freeing DNA frommodifications induced by formaldehyde, particularly cross-links topolypeptides. Reversing may be partial or complete and may or may notresult in restoration of DNA to its precise state beforeformaldehyde-induced modifications occurred.

DETAILED DESCRIPTION

Disclosed herein are methods, systems, compositions and kits forisolating nucleic acid from specimens preserved in liquid-based cytologypreservatives containing formaldehyde. Briefly, the disclosed approachrelies on contacting an aliquot of the sample, meaning the cellularsample disposed in the liquid preservative, with a combination of2-imidazolidone and a protease enzyme. In a highly preferred embodiment,the protease is the proteinase K enzyme. The mixture can then beincubated under conditions of high heat to inactivate free formaldehydeand reverse at least a portion of the chemical modifications of nucleicacid caused by formaldehyde. The approach advantageously is rapidcompared to prior methods, and results in nucleic acid, including RNA,that can be efficiently isolated (e.g., by capture probe hybridization),reverse transcribed (if desired) and amplified in vitro.

Introduction and Overview

The techniques disclosed herein facilitate detection of nucleic acidtargets that may be present in biological samples contained inliquid-based cytology preservatives that include formaldehyde. Suchbiological samples can be stored for substantial periods beforeundergoing analysis (e.g., at least 1, 2, 7, 14, 30, 50 or 100 days, or7-120 days). During storage, formaldehyde can induce modifications ofthe nucleic acids in the sample, particularly generation of cross-linkswith polypeptides present in the sample. These modification inhibitsubsequent processing of the DNA including its ability to hybridize(e.g., to a capture probe), or be amplified. Modifications, includingcross-links can be broken by a treatment with a protease, such asproteinase K. Treatment with a protease can increase the molecules ofnucleic acid available for capture and/or amplification and ultimatelyyield more amplification product and/or a lower threshold of detectionof a particular target. These beneficial effects of protease areincreased by concurrent treatment of the sample with 2-imidazolidone.The 2-imidazolidone acts as a formaldehyde scavenger, i.e., it reactswith formaldehyde in such a way as to render it incapable or at least ofsubstantially diminished ability to induce crosslinks between nucleicacids and polypeptides. Although 2-imidazolidone is used as an exemplaryand preferred formaldehyde scavenger in much of the description thatfollows, other formaldehyde scavengers, such as those described in theBackground can alternatively be used, and particularly so in embodimentsperformed at a temperature of 85° C. or higher unless the contextrequires otherwise. By removing reactive formaldehyde, the2-imidazolidone can inhibit polypeptides including polypeptides releasedby action of the protease from forming or reforming cross-links withnucleic acids in the sample. The 2-imidazolidone by removingformaldehyde can also protect the protease from inactivation. Although2-imidazolidone has previously been reported to be a formaldehydescavenger, it is surprising that its potential inhibition of formationof new cross-links for a short period of incubation results in materialimproved availability of nucleic acids for capture, amplification andsubsequent processing considering the long period of time for whichsamples may be stored and cross links can be formed before protease and2-imidazolidone are supplied. It is also surprising that presence of2-imidazolidone does not itself impair the ability of nucleic acids toundergo capture, amplification or other nucleic acid hybridization eventbecause some imidazolines are known nucleic acid denaturants.

The methods can be used on any form of nucleic acid including DNA andRNA. DNA can be genomic or cDNA among others. RNA can be mRNA, rRNA,hnRNA, tRNA, or viral RNA among others. While DNA may be the desiredanalyte, RNA presents more stringent requirements for sample processingdue to its chemical instability, including instability at hightemperatures. Thus, procedures for isolating RNA were pursued fordemonstrating the new method of sample preparation under the mostrigorous conditions.

A model system for gynecologic specimen collection using aformaldehyde-containing liquid-based cytology preservative was employedto illustrate the nucleic acid isolation technique. In its practicalapplication, this system involves first obtaining a swab of cervicalcells, transferring the obtained sample of cells to SUREPATH (aregistered trademark of TriPath Imaging, Inc.) liquid-based cytologypreservative, and then processing the preserved cells for subsequentmolecular testing. The molecular testing in this instance required invitro amplification and detection of human papillomavirus (HPV) RNAtarget nucleic acids.

HPV is associated with the development of cervical cancer, and thatdetection of expressed HPV RNA has particular value as a diagnostic andmonitoring assay. Indeed, HPV molecular testing in conjunction withcytology is now recommended for cervical cancer screening and patientmanagement. Accordingly, it was reasoned that liquid Pap testing wouldbe one example of an assay system that would benefit from enhancingrecovery of amplifiable RNA by improved processing of samples preservedin formalin, or other liquid-based cytology preservatives containingformaldehyde. Moreover, automated testing procedures based onamplification nucleic acid in vitro followed by detection ofHPV-specific amplification products would benefit as well.

The APTIMA® HPV genetic probe assay is a commercially availablemultiplex nucleic acid test that detects E6/E7 mRNA from 14 high-riskHPV genotypes (e.g., cat. no. 303585, Gen-Probe Incorporated, San Diego,Calif.). Among the genotypes detected are HPV 16, HPV 18, and HPV 45.This assay, which relies on target capture using a nucleic acidhybridization approach, has been demonstrated for use with cervicalspecimens preserved in THINPREP® liquid-based cytology preservative thatdoes not include formaldehyde. The genetic probe assay also has beendemonstrated for use with specimens preserved in SUREPATH® liquid-basedcytology reagent after being first combined with a specimen transportmedium (STM), and then treated with a reagent that includes relativelyhigh levels of proteinase K enzyme (180 U/reaction). SUREPATH®liquid-based cytology preservative contains formaldehyde, ethanol,methanol, and isopropanol. Whereas specimens preserved in THINPREP canbe processed rapidly for testing by the APTIMA® HPV genetic probe assay,specimens preserved in SUREPATH® require digestion with proteinase K fortwo hours at 65° C. This requirement compromises the utility of thelatter preservative. By the improved method described below, specimenspreserved in SUREPATH® liquid-based cytology reagent can be processedusing less enzyme reagent and an incubation time of only 15 minutes.

Preferred Reagent Compositions

The disclosed technique for preparation of nucleic acid fromformaldehyde-containing liquid-based cytology preservatives relies onthe combined use of a protease enzyme and 2-imidazolidone. The disclosedtechnique further relies upon use of a protease enzyme at a hightemperature. In a preferred approach, the protease enzyme begins in alyophilized form that is reconstituted using a buffered solution thatincludes 2-imidazolidone. Preferably, the reconstitution buffer furtherincludes EDTA. In one highly preferred embodiment, the protease enzymeis the proteinase K enzyme, which is known to retain activity within thebroad range of pH 4.0-pH 12.0. However, the pH of the buffer used forreconstituting protease enzyme preferably falls in the range of fromabout pH 7.5 to about pH 8.5. This range permits optimal enzymaticactivity while still protecting RNA from hydrolytic cleavage that occursunder strongly alkaline conditions. Still more preferably, the bufferused in the reconstitution buffer includes a Tris buffer at about pH8.0.

The final concentrations of key reagent components, when combined withan optional diluent and the liquid-based cytology preservative thatincludes formaldehyde, fall within preferred ranges. The optionaldiluent can be a buffered solution that includes a detergent that lysescell membranes. Exemplary detergents include anionic detergents such assodium dodecyl sulfate (SDS), and lithium lauryl sulfate (LLS). Otherdetergents, such as the nonionic detergents, may also be useful.Advantageously, the strong ionic detergents can denature proteins,thereby rendering them better targets for proteolysis by the proteinaseK enzyme. The final concentration (by molarity) of 2-imidazolidine inthe reaction mixture preferably is selected to fall in a range that is1-fold to 5-fold, or more preferably 2-fold to 5-fold the final maximumconcentration of formaldehyde. Final concentration of 2-imdazolidone isdetermined the moles added over the volume of the reaction mixture afterall reagents have been added. Final concentration of formaldehyde is theamount of moles present in the preservative used for making the specimendivided by the volume of the reaction mixture after all reagents havebeen added. In other words, no subtraction is made for formaldehydeconsumed in inducing crosslinks before the heat incubation. For example,if a reaction mixture prepared by combining 1 ml of liquid-basedcytology preservative (e.g., including a cellular specimen), 2.9 ml of adiluent, and 0.3 ml of a reagent including 2-imidazolidone, proteinase Kenzyme, EDTA, and buffer had a final formaldehyde concentration of about28 mM, then the final concentration of 2-imidazolidone at about 2-foldexcess would be about 50 mM to about 60 mM. The final concentration ofproteinase K enzyme advantageously can be reduced in the presentformulation relative to the amount that would otherwise be used in theabsence of 2-imidazolidone. Although practice of the invention is notdependent on an understanding of any particular mechanism of action, itis believed that proteinase K may serve to digest amine bonds connectingproteins to methyl bridges, thereby releasing nucleic acid and making itaccessible for target capture in the hybridization-dependent targetcapture step of the APTIMA® assay. The final concentration of proteinaseK enzyme preferably falls in the range of from about 43 U/ml to about4.3 U/ml, with a concentration of about 10-11 U/ml being highlypreferred. Thus, a reaction volume of 4.2 ml would preferably includeabout 40-50 U or 43 U of proteinase K enzyme. The final concentration ofEDTA preferably falls in the range of from 10 mM to 100 mM, morepreferably in the range of from 10 mM to 50 mM, and still morepreferably in the range of from 30 mM to 40 mM. The final concentrationof buffering agent is variable, based on the structure of the agent, butis sufficient to provide adequate buffer capacity to ensure RNAcontained in the sample is not substantially degraded by alkalinehydrolysis. This requirement can be fulfilled by employing a finalbuffer concentration in the range of from at least 10 mM up to about 500mM, more preferably up to about 250 mM, still more preferably up toabout 100 mM, and yet still more preferably up to about 50 mM. A highlypreferred final concentration range for buffer in the reaction mixtureprior to incubation at elevated temperature is 10 mM to 50 mM.

The specimen can be combined with protease and 2-imidazolidone in anyorder. For example, the protease and 2-imidazolidone can be combinedwith the specimen simultaneously. Alternatively, the protease can becombined with the specimen first, followed by 2-imidazolidone, or vice aversa.

Both of the reconstitution buffer and lyophilized protease may becomponents of a kit, and may be combined shortly before use. That is tosay, an end-user of the kit may reconstitute the lyophilized enzyme toprepare the enzyme reagent that includes, for example, 2-imidazolidone,proteinase K enzyme, EDTA, and pH buffer. Preferably, a single solutionof the reagent kit includes 2-imidazolidone, EDTA, and pH buffer, butdoes not include the proteinase K enzyme. The proteinase K enzymepreferably is packaged in a separate vial of the kit, where the enzymeis in the form of a lyophilisate.

Preferred Target Enrichment Approaches

Before initiating the amplification reaction, it may be desirable tofirst enrich or isolate target nucleic acids using a target capturetechnique. In a preferred approach, nucleic acids from the reactionmixture incubated at elevated temperature following addition of areagent including 2-imidazolidone and proteinase K enzyme are contactedwith a solid support having disposed thereon an immobilized probe.According to one embodiment, target nucleic acids having been processedby treatment with the combination of 2-imidazolidone and protease enzymeunder elevated temperature conditions in the presence of EDTA and a pHbuffer hybridize directly to the immobilized capture probe in asequence-specific fashion. In a different embodiment, a “target captureprobe” serves to bridge the solid support-immobilized capture probe andthe target nucleic acid that is to be amplified. General features ofthis approach are disclosed by Weisburg et al., in U.S. Pat. No.6,534,273, the disclosure of this document being incorporated byreference herein. Regardless of which approach is chosen, it should beclear that hybridization involving the target nucleic acid that is to beamplified is an essential feature of the procedure.

A variant target capture approach that may be used in connection withthe techniques disclosed herein, and that relies on nonspecifichybridization to the target that is to be amplified, is detailed inpublished U.S. patent application U.S. 2008/0286775 A1, the disclosureof this document being incorporated by reference herein. In accordancewith the nonspecific hybridization approach, the capture probe includesat least one sequence that exhibits alternative base pairing propertiesfor the target nucleic acid compared to standard base pairing (i.e., G:Cand A:T/U bonding). The target nucleic acid purified by this nonspecifichybridization approach may be RNA or DNA, which is at least partiallysingle-stranded. Again, it should be clear that thissequence-independent target capture approach still relies on nucleicacid hybridization.

The present data show that target capture can occur notwithstanding thepresence of 2-imidazolidone and reports that some imidazolines causedenaturation of nucleic acids.

Preferred Nucleic Acid Amplification Methods

Examples of amplification methods useful in connection with the presentinvention include, but are not limited to: transcription mediatedamplification (TMA), single-primer nucleic acid amplification, nucleicacid sequence-based amplification (NASBA), the polymerase chain reaction(PCR), strand displacement amplification (SDA), self-sustained sequencereplication (3SR), DNA ligase chain reaction (LCR) and amplificationmethods using self-replicating polynucleotide molecules and replicationenzymes such as MDV-1 RNA and Q-beta enzyme. Methods for carrying outthese various amplification techniques respectively can be found in U.S.Pat. No. 5,399,491, U.S. patent application Ser. No. 11/213,519,published European patent application EP 0 525 882, U.S. Pat. No.4,965,188, U.S. Pat. No. 5,455,166, Guatelli et al., Proc. Natl. Acad.Sci. USA 87:1874-1878 (1990), International Publication No. WO 89/09835,U.S. Pat. No. 5,472,840 and Lizardi et al., Trends Biotechnol. 9:53-58(1991). The disclosures of these documents which describe how to performnucleic acid amplification reactions are hereby incorporated byreference.

Reaction Mechanism

Although practice of the present methods is not depending on anunderstanding of mechanism, FIG. 6 illustrates a possible reactionmechanism underlying the methods. Under acidic conditions, formaldehyde2 in a specimen can react with the nucleophilic functional groups ofeither nucleotides or polypeptides. Elimination of water then generatesa reactive imine 4. A second nucleotide can then react with the imine toform the dimer 5. Proteinase K, which is a serine protease, hydrolyzesand cleaves the nitrogen-methylene linker. This cleavage can regeneratethe starting nucleotides and formaldehyde. 2-imidazolidone, which is aformaldehyde scavenger, can react with two molecules of formaldehyde togenerate an imidazolidone-methanol compound 7. This reaction effectivelyprevents the formaldehyde from reacting again with either the releasednucleotides or polypeptides.

Sensitivity

Treatment of a specimen with a protease and 2-imidazolidone as justdescribed can result in reversal of more modifications, particularlycross-links, on nucleic acids in the sample, more nucleic acids beingfreed from cross-linked polypeptides, greater yield of captured nucleicacid, greater yield of amplified nucleic acids, and improved assaysensitivity (i.e., lower threshold of a target DNA needed to be presencefor a target). Such improvements can be measured relative to otherwisecomparable controls in which the protease or the 2-imidazolidone or bothis/are omitted. Preferably improvement is shown compared both with acontrol in which the protease is omitted and with a control in which the2 imidazolidone is omitted. Improvement means an improvement ofsufficient magnitude to make it beyond typical experimental variation(p<0.05). For example, in some methods, treatment can result in animprovement of at least 5%, 10%, 20%, or 30% of yield of nucleic acidsfreed from cross-links or captured nucleic acids or amplified nucleicacids. Presence of cross-links can be assessed by assays separating bymolecular weight such as gel electrophoresis or various forms of columnchromatography. In some methods, treatment results in at least 50, 60,70, 80 or 90% of nucleic acid molecules being free of cross-links topolypeptides and thus potentially subject to a hybridization captureassay or amplification. In some methods, treatment results in a higherassay positivity (or lower threshold of detection) meaning that somesamples yield a positive result (target nucleic acid present) aftertreatment in accordance with the present methods than in controltreatments in which either protease or 2-imidazolidone is omitted.

Preferred Embodiments

The following Examples disclose experimental procedures carried out todemonstrate the benefits of treating specimens in aformaldehyde-containing liquid-based cytology preservative with thecombination of 2-imidazolidone and proteinase K enzyme at an elevatedtemperature. In a preferred embodiment, this combination is used in thepresence of Tris buffer and EDTA. In all instances, the SUREPATHliquid-based cytology preservative served as the model liquid-basedpreservative containing formaldehyde. In the descriptions that follow,“demodifier solution” refers to a pH-buffered solution (pH 8.0) thatincluded EDTA (500 mM) and 2-imidazolidone (in the range of from 740 mMto 750 mM). Preferred buffers for use in the demodifier solution includeTris buffer. As used herein, “specimen transport medium” (STM) refers toa phosphate-buffered detergent solution which, in addition to lysingcells, protects released RNAs by inhibiting the activity of RNases thatmay be active in the sample undergoing testing. Preferred detergentsthat may be used in STM include sodium dodecyl sulfate (SDS) and lithiumlauryl sulfate (LLS), with LLS being slightly more preferred. Whensamples of liquid-based cytology preservative containing formaldehydeare to be combined with the demodifier solution and proteinase K enzyme,lyophilized enzyme conveniently can be reconstituted with the demodifiersolution, and an aliquot of the reconstituted enzyme solution can beadded to a reaction vessel containing the liquid-based cytologypreservative.

Example 1 describes procedures used to assess analytical sensitivity ofthe experimental system by testing panels that included in vitrotranscripts for each of the 14 high risk HPV genotypes. Success of thenucleic acid processing technique involving treatment with2-imidazolidone and proteinase K under elevated temperature conditionswas measured by detection of HPV RNA using a commercially availableassay. As indicated below, results showed that the treatment conditionsdid not compromise amplification and detection of HPV RNAs.

EXAMPLE 1 Establishing Analytical Sensitivity of the HPV Assay UsingSynthetic Transcripts

In vitro synthesized transcripts served as templates for amplificationin conventional TMA reactions performed using the APTIMA® HPV geneticprobe assay for amplification and detection of HPV RNA. The transcriptcopy number used for each different HPV type corresponded to the limitof detection (LOD) for the APTIMA HPV genetic probe assay that had beenestablished in preliminary procedures using specimens preserved inTHINPREP liquid-based cytology preservative (i.e., the modelpreservative that does not contain formaldehyde). The LOD is the copylevel that leads to a minimum positivity of at least 95% for allspecimens tested. In this instance, in vitro transcripts were all usedat 20 to 600 copies/reaction, as appropriate.

Three different sample processing conditions were tested. First, invitro transcripts were added to THINPREP® liquid-based cytology samplesin STM (1 ml sample and 2.9 ml STM), and then processed according todirections from the manufacturer of the APTIMA® HPV genetic probe assay.Second, in vitro transcripts were added to clinical HPV-negativeresidual SUREPATH liquid-based cytology preservative specimens in STM (1ml sample and 2.9 ml STM). Aliquots (3.9 ml each) of the mixture werecombined with 100 μl of a proteinase K reagent (1.8 U/μl proteinase K inTris buffer (pH 8.0), sodium azide, and CaCl₂), and then incubated for 2hours at 65° C. Following the enzyme digestion step, the mixtures wereprocessed according to directions from the manufacturer of the APTIMAHPV genetic probe assay. Finally, as in the second case, in vitrotranscripts were added to clinical HPV-negative residual SUREPATHliquid-based cytology preservative specimens in STM. In this instance,3.9 ml aliquots of each sample STM mix were combined with 0.3 ml of aproteinase K enzyme reagent that included 2-imidazolidone in Tris-EDTAbuffer. This reagent had been prepared by reconstituting lyophilizedproteinase K using the demodifier solution. The final mixtures included36 mM EDTA, 36 mM Tris-HCl, about 53 mM 2-imidazolidone, and 43 U ofproteinase K enzyme. Mixtures were incubated at 90° C. for 15 minutes,and then processed according to directions from the manufacturer of theAPTIMA® HPV genetic probe assay. Following amplification and detectionof HPV RNA, the frequency of positive HPV detection was compared amongreplicates.

FIG. 1 shows the results of the analytical sensitivity evaluationperformed using in vitro transcripts. Assay positivity for the samplespreserved in SUREPATH liquid-based cytology preservative was at least95% for 11 of the 14 HPV genotypes; with 3 genotypes, HPV 56, 58 and 59yielding 93.3, 91.7 and 90% positivity, respectively. These results weresimilar to those obtained for samples preserved in THINPREP liquid-basedcytology preservative, and similar or better than samples that had beenpreserved in SUREPATH liquid-based cytology preservative and thentreated with proteinase K enzyme alone. This established the utility ofthe HPV testing system, and showed that use of the combination of2-imidazolidone and proteinase K enzyme under elevated temperatureconditions did not substantially inhibit in vitro amplification anddetection reactions.

Example 2 describes procedures used for assessing analytical sensitivityof the HPV assay by testing a panel of human cells containing HPV.Procedures were generally as described under Example 1, except that: (1)HPV-expressing cell lines were used in place of in vitro transcripts;and (2) the samples were incubated in the presence of theformaldehyde-containing preservative for an extended period.

EXAMPLE 2 Establishing Analytical Sensitivity of the HPV Assay UsingHuman Cell Lines Containing HPV

Human cell lines containing HPV were spiked into specimen pools of theSUREPATH liquid-based cytology preservative, stored for 7 days at 25°C., and then tested at half-log dilutions (3 to 30 cells/reaction) aftertreatment with either the combination of the demodifier solution andproteinase K at 90° C. for 15 minutes, or proteinase K alone at 65° C.for 2 hours. As in Example 1, the combination of demodifier solution andproteinase K was conveniently delivered as a single aliquot byreconstituting lyophilized proteinase K with the demodifier solution. Ofcourse, there is no requirement for combining the reagents in thisfashion. Cells used in this procedure were: (1) SiHa cells (expressingHPV16); (2) HeLa cells (expressing HPV 18); and (3) MS751 cells(expressing HPV 45). Again, HPV nucleic acids were captured, amplifiedand detected using the APTIMA HPV genetic probe assay in accordance withthe manufacturer's instructions. The positivity of samples treated underthe two conditions was compared.

FIGS. 2A-2C show the analytical sensitivity results obtained using celllines that had been stored for 7 days at 25° C. in SUREPATH liquid-basedcytology preservative. Assay positivity for all three HPV-positive celllines in samples treated with the combination of the demodifier solutionand proteinase K enzyme was at least 95% at concentrations of 30, 10 and30 cells/reaction for SiHa, HeLa and MS751 cells, respectively. Theseresults were similar or better than results obtained using samples thathad been stored 7 days at 25° C. in SUREPATH liquid-based cytologypreservative and then treated with proteinase K enzyme alone. The mostdramatic differences were observed in the trials using HeLa cells at thelowest input cell count. There was a clear statistically significantadvantage to the sample processing treatment using 2-imidazolidone incombination with proteinase K and high temperature.

Example 3 describes procedures that demonstrated how the combined use of2-imidazolidone and proteinase K under elevated temperature conditionsled to improved recovery of amplifiable nucleic acid from samples storedfor extended periods in a liquid-based cytology preservative containingformaldehyde. As discussed below, the difference in RNA recoveryrelative to trials treated with proteinase K alone was most noticeableat extended time periods.

EXAMPLE 3 Enhancing Recovery of Amplifiable mRNA from Cellular SpecimensStored in a Liquid-Based Cytology Preservative Containing Formaldehyde

To mimic clinical specimens, ten pools of residual specimens in SUREPATHliquid-based cytology preservative, previously determined to beHPV-negative using the APTIMA HPV genetic probe assay, were split inhalf and spiked with either SiHa or HeLa cells. All tubes were storedneat at 25° C. for up to 42 days. Aliquots from each pool were dilutedin a 1:2.9 SUREPATH:STM matrix to final cell concentrations of 30 and100 cells/reaction on each day of testing. Samples were processed eitherby treatment with proteinase K alone for 2 hours at 65° C., or with thecombination of demodifier solution and proteinase K (the combinationbeing delivered as a single aliquot of proteinase K reconstituted withdemodifier solution) for 15 minutes at 90° C. Again, HPV nucleic acidswere captured, amplified and detected using the APTIMA HPV genetic probeassay in accordance with the manufacturer's instructions.

FIGS. 3A-3B present results supporting the advantages of sampleprocessing that included treatment with the combination of2-imidazolidone and proteinase K under elevated temperature conditions,relative to treatment with proteinase K alone. All results during thisstudy were valid. At 30 cells per reaction, both SiHa and HeLa cellstreated with the combination of 2-imidazolidone and proteinase K (e.g.,proteinase K reconstituted with demodifier solution) maintained 100%positivity out to Day 14. Beyond this storage period, the combinationtreatment enhanced recovery of amplifiable RNA to a greater extent thantreatment with proteinase K alone. At 100 cells/reaction, HeLa cellsmaintained 100% positivity out to Day 28, while SiHa cells remain 100%positive until Day 21 (data not shown).

Example 4 describes the procedure used to demonstrate that clinicalsamples stored in a formaldehyde-containing liquid-based cytologypreservative could be treated with the combination of 2-imidazolidoneand proteinase K under elevated temperature conditions and thenprocessed to yield substantially constant amounts of RNA, regardless ofthe length of time the clinical sample had been stored.

EXAMPLE 4 Combination Treatment Permits Efficient Recovery of RNA forClinical Samples Over Extended Storage Periods

Thirty verified HPV-positive clinical specimens in SUREPATH liquid-basedcytology preservative, obtained from a referral population, wereevaluated in this study. An aliquot (0.5 ml) of each specimen was addedto 2.9 ml STM and then diluted 1:10 and 1:100 in a 0.5:2.9 SP:STMmatrix. Dilutions were stored at 4° C. and then tested at various timepoints for 120 days with the APTIMA HPV genetic probe assay (N=4 foreach sample, 120 total replicates per time point). On each day oftesting, 1 ml aliquots of the samples were mixed with 2.9 ml of STM and0.3 ml of a reagent that included proteinase K reconstituted indemodifier solution to a final concentration of 143 U/ml of proteinaseK. Mixtures were incubated at 90° C. for 15 minutes, processed toisolate nucleic acids by a target capture protocol, and tested with theAPTIMA HPV genetic probe assay on an automated testing instrument.

FIG. 4 presents results showing that clinical specimens preserved in aliquid-based cytology preservative containing formaldehyde could betreated with the combination of 2-imidazolidone and proteinase K underelevated temperature conditions for a short time period to result insubstantially constant recovery of RNA. All specimens that had beendiluted 1:10 maintained at least 97.5% positivity after 120 days ofstorage at 4° C. Positivity for all 30 specimens diluted 1:100 rangedfrom 74.2% to 87.5% over the course of the study, with no consistentdecrease in positivity observed.

EXAMPLE 5 Temperature Dependence

Target preparation: Tubes containing HPV18-infected HeLa cells werethawed at 37° C. and pooled into one tube. Phosphate-buffered saline wasadded to the tube and the tube was spun in a centrifuge at 1100 rcf toform a cell pellet. The supernatant was removed by pipetting. A pool ofHPV-negative SurePath® clinical specimen derived from cell pellets(NCPP) was added to simulate a SurePath clinical specimen. The tubecontaining HeLa cells and NCPP was inverted to break up the pellet andincubated at 25° C. (concentration: 1000 cells/mL). After 0, 7, and 14days, an aliquot from the tube was removed, STM was added, and dilutionswere performed to a final concentration of 10 cells/reaction (finalratio of NCPP:STM 1:2.9). Tubes were treated (see next section) andtested using an APTIMA® HPV kit according to manufacturer'sinstructions.

Treatment methods: After 25° C. incubation and STM addition (seeprevious section) tubes were divided into 3 groups. Heat: 300 μL TE(concentration in tube: 36 mM Tris, 36 mM EDTA) was added to reactiontubes. Tubes were capped, placed in a 90° C. water bath for 15 minutes,and tested on APTIMA HPV. PK: 50 mg proteinase K was dissolved in 1 mLFast Express diluent. 100 μL of the PK solution was added to reactiontubes (180 units proteinase K per tube). Tubes were capped, placed in a65° C. water bath for 2 hours, and tested on APTIMA HPV. Heat+PK: 50 mgproteinase K was dissolved in 12 mL TE. 300 μL of the TE+PK solution wasadded to reaction tubes (concentration in tube: 36 mM Tris, 36 mM EDTA,45 units PK). Tubes were capped, placed in a 90° C. water bath for 15minutes, and tested an APTIMA® HPV kit according to manufacturer'sinstructions. Results are presented in Table 1.

TABLE 1 Time Point Heat PK Heat + PK D 0 100%  100%  100%  D 7 60% 85%90% D 14 25% 50% 75% N = 20

These data indicates that the combined treatment was most effective onsamples having undergone the longest storage. Moreover, samples treatedwith proteinase K at a high temperature resulted in a greater recoverythat did those treated with proteinase K at low temperature or treatedwith a high temperature alone.

EXAMPLE 6 Formaldehyde Scavengers, Proteinase K and High Temperature

Targets were prepared substantially as described above in Example 5.Briefly, HeLa cell lines (HPV-18+), SiHa cell lines (HPV-16+), MS751cell lines (HPV-45+) and Trichomonas cell lines (Trichomonas+) wereincubated for 7 days in SurePath solution. After 7 days an aliquot ofeach SurePath cell sample was then combined into a condition asillustrated in Table 2.

TABLE 2 Condition Formulation* 1 Proteinase K 2 Proteinase K andTris/EDTA 3 Proteinase K, Tris/EDTA and 1X 2-Imidazolidone** 4Proteinase K, Tris/EDTA and 2X 2-Imidazoladone** 5 Proteinase K,Tris/EDTA and succinic acid dihydrazide *HeLa and SiHa cells wereincubated in the presence of 180 U proteinase K and in the presence of45 U proteinase K. **1X and 2X refer to the molar concentration of2-imidazolidone in the solution. 1X means that the molar concentrationwas about equivalent to that of the formaldehyde in the solution; 2Xmeans it was twice that of formaldehyde.

The combined solutions were then incubated for either 15 minutes or for2 hours and at a temperature of either 65° C. or 90° C. Incubationconditions are illustrated in Table 3.

TABLE 3 Treatment Cell Line Condition Temperature Time 1 HeLa 1 65° C. 2hours 2 HeLa 2 90° C. 15 minutes 3 HeLa 3 90° C. 15 minutes 4 HeLa 4 90°C. 15 minutes 5 HeLa 5 90° C. 15 minutes 6 SiHa 1 65° C. 2 hours 7 SiHa2 90° C. 15 minutes 8 SiHa 3 90° C. 15 minutes 9 SiHa 4 90° C. 15minutes 10 SiHa 5 90° C. 15 minutes 11 MS715 1 65° C. 2 hours 12 MS715 290° C. 15 minutes 13 MS715 5 90° C. 15 minutes 14 Trichomonas 1 65° C. 2hours 15 Trichomonas 2 90° C. 15 minutes 16 Trichomonas 4 90° C. 15minutes

Following incubations, the samples were assayed to determine nucleicacid recovery under the various treatments. In a first assay, 3cells/reaction of HeLa cells from conditions 1-4 and 10 cells/reactionof SiHa cells from conditions 1-4 (see Table 3) were assayed using anAPTIMA HPV kit (catalog no. 303585, Gen-Probe Incorporated) generallyaccording to manufacturer's instructions. In a second assay, 0.05cells/reaction of Trichomonas cells from conditions 1, 2 & 4 (see Table3) were assayed using an APTIMA Trichomonas vaginalis assay (catalog no.303563, Gen-Probe Incorporated) generally according to manufacturer'sinstructions. In a third assay, 3 cells/reaction of each of HeLa, SiHaand MS751 cells from conditions 1, 2 & 5 (See Table 3), each incubatedwith 45 U of proteinase K, were assayed using an APTIMA HPV kit (catalogno. 303585, Gen-Probe Incorporated) generally according tomanufacturer's instructions. In a fourth assay, 3 cells/reaction of eachof HeLa, SiHa and MS751 cells from conditions 1, 2 & 5 (See Table 3),each incubated with 45 U of proteinase K, were assayed using an APTIMAHPV genotyping kit (catalog no. 303234, Gen-Probe Incorporated)generally according to manufacturer's instructions. Results arepresented in Tables 4 to 7.

TABLE 4 HPV Detection Assay and 180 U Proteinase K First Cell % AssayTreatment Line Condition Temp Time Positive 1 HeLa 1 65° C. 2 hours  33%2 HeLa 2 90° C. 15 minutes 73% 3 HeLa 3 90° C. 15 minutes 78% 4 HeLa 490° C. 15 minutes 83% 6 SiHa 1 65° C. 2 hours  80% 7 SiHa 2 90° C. 15minutes 83% 8 SiHa 3 90° C. 15 minutes 92% 9 SiHa 4 90° C. 15 minutes90%

TABLE 5 Trichomonas vaginalis Assay and 180 U Proteinase K % SecondTreat- Cell Condi- Pos- Assay ment Line tion Temp Time itive 14Trichomonas 1 65° C. 2 hours  33% 15 Trichomonas 2 90° C. 15 minutes 67%16 Trichomonas 4 90° C. 15 minutes 97%

TABLE 6 HPV Detection Assay and 45 U of Proteinase K Third Treat- Cell %Assay ment Line Condition Temp Time Positive 1 HeLa 1 65° C. 2 hours 30% 2 HeLa 2 90° C. 15 minutes 40% 5 HeLa 5 90° C. 15 minutes 85% 6 SiHa1 65° C. 2 hours  75% 7 SiHa 2 90° C. 15 minutes 70% 10 SiHa 5 90° C. 15minutes 90% 11 MS715 1 65° C. 2 hours  15% 12 MS715 2 90° C. 15 minutes30% 13 MS715 5 90° C. 15 minutes 30%

TABLE 7 HPV Genotyping Assay and 46 U of Proteinase K Fourth Treat- Cell% Assay ment Line Condition Temp Time Positive 1 HeLa 1 65° C. 2 hours 30% 2 HeLa 2 90° C. 15 minutes 40% 5 HeLa 5 90° C. 15 minutes 85% 6 SiHa1 65° C. 2 hours  75% 7 SiHa 2 90° C. 15 minutes 70% 10 SiHa 5 90° C. 15minutes 90% 11 MS715 1 65° C. 2 hours  15% 12 MS715 2 90° C. 15 minutes30% 13 MS715 5 90° C. 15 minutes 30%

These data show that specimens preserved in a liquid-based cytologypreservative containing formaldehyde could be treated with thecombination of a formaldehyde scavenger, proteinase K and an elevatedtemperature for a short time period to result in substantially constantrecovery of RNA. These data further show formulations containingproteinase K that are useful at high temperatures known to denature andinactivate proteinase K and further known to destroy RNA, and yetprovide superior nucleic acid recovery compared to recovery at lowertemperatures. These data further show that formulations that allow forrecovery of nucleic acids from a formalin containing solution using areduced concentration of protease.

EXAMPLE 7

The following assay was performed to determine the percent recovery ofRNA from samples that had been treated for 7 days with a SurePath®reagent, the samples being treated with proteinase K for 15 minutes at anumber of high temperatures. Samples were prepared substantially asdescribed in Example 6. Briefly, HeLa cell lines (HPV-18+) and SiHa celllines (HPV-16 +) were incubated for 7 days and at 25° C. in Surepath®.After 7 days and aliquot of each SurePath® cell sample was then combinedinto condition 3 as illustrated in Table 2, above. The combinedsolutions were then incubated at a number of temperatures for 15 minutesand assayed using an HPV detection kit (catalog no. 303585, Gen-ProbeIncorporated), as presented in Table 8.

TABLE 8 % Positive HeLa @ % Positive SiHa @ Temperature 3 cells/reaction10 cells/reaction 85° C. 88% 95% 90° C. 85% 93% 95° C. 98% 95%

The following assay was performed to determine the percent recovery ofRNA from samples that had been treated for 7 days with a SurePath®reagent, the samples being treated with proteinase K at 90° C. for anumber of short incubation times. Samples were prepared substantially asdescribed in Example 6. Briefly, HeLa cell lines (HPV-18+) and SiHa celllines (HPV-16+) were incubated for 7 days and at 25° C. in Surepath®.After 7 days and aliquot of each SurePath® cell sample was then combinedinto condition 3 as illustrated in Table 2, above. The combinedsolutions were then incubated at 90° C. for a number of minutes, andthen assayed using an HPV detection kit (catalog no. 303585, Gen-ProbeIncorporated), as presented in Table 9.

TABLE 9 % Positive HeLa @ % Positive SiHa @ Time 3 cells/reaction 10cells/reaction 13 minutes 80% 93% 15 minutes 85% 93% 17 minutes 93% 90%20 minutes 95% 95%

The following assay was performed to determine the percent recovery ofRNA from samples that had been treated for 7 days with a SurePath®reagent, the samples being treated with a number of concentrations ofproteinase K at 90° C. for a 15 minute incubation time. Samples wereprepared substantially as described in Example 6. Briefly, HeLa celllines (HPV-18+) and SiHa cell lines (HPV-16+) were incubated for 7 daysand at 2° C. in Surepath®. After 7 days and aliquot of each SurePathcell sample was then combined into condition substantially likecondition 3 illustrated in Table 2, above, with the exception that theproteinase K concentrations listed in Table C. The combined solutionswere then incubated at 90° C. for 15 minutes, and then assayed using anHPV detection kit (catalog no. 303585, Gen-Probe Incorporated), aspresented in Table 10.

TABLE 10 % Positive HeLa @ % Positive SiHa @ U of proteinase K 3cells/reaction 10 cells/reaction 39.6 U 83% 90% 43.0 U 83% 93% 46.4 U85% 90%

The following assay was performed to determine the percent recovery ofRNA from samples that had been treated for 7 days with a SurePathreagent, the samples being treated with a number of concentrations of2-imidazolidone at 90° C. for a 15 minute incubation time. Samples wereprepared substantially as described in Example 6. Briefly, HeLa celllines (HPV-18+) and SiHa cell lines (HPV-16+) were incubated for 7 daysand at 25° C. in Surepath. After 7 days and aliquot of each SurePathcell sample was then combined into condition substantially likecondition 3 illustrated in Table 2, above, with the exception that the2-imidazolidone concentrations listed in Table D. The combined solutionswere then incubated at 90° C. for 15 minutes, and then assayed using anHPV detection kit (catalog no. 303585, Gen-Probe Incorporated), aspresented in Table 11.

TABLE 11 % Positive HeLa @ % Positive SiHa @ mM 2-imidazolidone 3cells/reaction 10 cells/reaction 26.6 mM 78% 95% 47.9.mM 80% 93% 53.2 mM83% 93% 58.6 mM 75% 90% 106.5 mM  75% 90%For all assays, the number of replicates was 40

EXAMPLE 8 Work Flow Incorporating Processing of Specimens Preserved in aLiquid-Based Cytology Preservative that Includes Formaldehyde

Example 8 describes a typical work flow for processing clinical samples.A clinical sample obtained using a swab device is introduced into a vialcontaining a liquid-based cytology preservative that includesformaldehyde, and the vial is capped securely. SUREPATH liquid-basedcytology preservative can be used as the liquid-based cytologypreservative. Cellular material dispersed in the liquid contents of thevial is transported to a clinical laboratory for testing, includingmolecular analysis of nucleic acid. At the clinical laboratory analiquot of the vial is mixed with an aliquot of a diluent, such as abuffered detergent solution. A phosphate-buffered detergent solution isone example of a preferred diluent. The detergent used in thisapplication preferably is an anionic detergent, such as sodium dodecylsulfate (SDS) or lithium lauryl sulfate (LLS). The mixture is furthercombined with 2-imidazolidone and a protease. The protease used for thispurpose may be the proteinase K enzyme. In a simplified approach,lyophilized proteinase K is reconstituted in a solution that includes apH buffer, EDTA, and 2-imidazolidone. The pH buffer may be a Trisbuffer, and the reconstituted enzyme solution may have a pH of about8.0. The final mixture that includes the diluted clinical sample, the2-imidazolidone and the protease enzyme is then heated to an elevatedtemperature for between 5 minutes and 30 minutes. The mixture ispreferably heated to about 90° C. for about 15 minutes. Nucleic acid inthe sample is rendered suitable for purification and use as a templatein an in vitro amplification reaction. For example, RNA is purified bycapture onto a solid support, for example using sequence-specifichybridization to an immobilized nucleic acid strand, and then amplifiedin a nucleic acid amplification reaction. The nucleic acid amplificationreaction may be a Transcription Mediated Amplification (TMA) reaction.Amplification products are contacted with a sequence-specifichybridization probe to determine the presence or absence of a particulartarget sequence. The particular target sequence may be an HPV targetsequence. The workflow is depicted in FIG. 5.

This invention has been described with reference to a number of specificexamples and embodiments thereof. Of course, a number of differentembodiments of the present invention will suggest themselves to thosehaving ordinary skill in the art upon review of the foregoing detaileddescription. Thus, the true scope of the present invention is to bedetermined upon reference to the appended claims. Unless otherwiseapparent from the context, any embodiment, aspect, step or feature ofthe invention can be used with any other.

1. A method of isolating a nucleic acid from a specimen that includes aclinical sample disposed in a liquid-based cytology preservative thatcomprises formaldehyde, the method comprising the steps of: (a)combining the specimen with a protease enzyme and formaldehyde scavengerto create a reaction mixture; (b) incubating the reaction mixture at anelevated temperature for a period of time sufficient to reverse chemicalmodifications of nucleic acid that may be contained in the specimen byformaldehyde in the liquid-based cytology preservative; and (c)isolating a nucleic acid from the reaction mixture after the incubatingstep.
 2. The method of claim 1, wherein the formaldehyde scavenger is2-imidazolidone.
 3. The method of claim 1, wherein the reversingreleases nucleic acids in the specimen from formaldehyde-inducedcrosslinking to polypeptides in the specimen.
 4. The method of claim 3,wherein the protease enzyme frees the nucleic acids from theformaldehyde-induced crosslinking.
 5. The method of claim 1, wherein theclinical sample has been disposed in the liquid-based cytologypreservative for from about 7 to about 120 days before performing step(a).
 6. The method of claim 1, wherein the incubating step is for aperiod of time no greater than 30 minutes; or is for a period of timebetween about 5 minutes and 30 minutes; or is for a period of time nogreater than 15 minutes; or is for a period of time between about 5minutes and 15 minutes. 7.-10. (canceled)
 11. The method of claim 1,wherein at least 90% of the chemical modifications of the nucleic acidmolecules in the specimen are reversed after the incubating step. 12.The method of claim 2, wherein final concentration of 2-imidazolidonebefore the incubation step is from about 1 to about 5 fold by molesgreater than the final maximum concentration of the formaldehyde. 13.(canceled)
 14. The method of claim 12, wherein the protease enzyme isproteinase-K present at a concentration of from about 4.3 to about 43U/ml.
 15. The method of claim 1, wherein the temperature of theincubating step is from about 60° C. to about 100° C.; or is from about85° C. to about 95° C.; or is from about 91° C. to about 95° C.; or isabout 90° C. 16.-18. (canceled)
 19. The method of claim 1, wherein theprotease enzyme and formaldehyde scavenger are combined simultaneouslywith the specimen.
 20. The method of claim 1, wherein the proteaseenzyme is combined with the specimen before formaldehyde scavenger. 21.The method of claim 1, wherein the formaldehyde scavenger is combinedwith the specimen before the protease enzyme. 22.-23. (canceled)
 24. Themethod of claim 1, wherein the clinical sample comprises RNA. 25.(canceled)
 26. The method of claim 24, wherein the isolated nucleic acidis RNA.
 27. The method of claim 1, wherein the nucleic acid is isolatedin step (c) by a target capture assay with a target capture probehybridizing to the nucleic acid to be isolated and to an immobilizedprobe that is immobilized to a solid support, preferably a magnetic beadsolid support. 28.-31. (canceled)
 32. The method of claim 24, whereinthe isolated nucleic acid is human papillomavirus (HPV) RNA targetnucleic acid.
 33. The method of claim 1, wherein the specimen is acervical cell clinical sample disposed in a liquid-based cytologypreservative. 34.-42. (canceled)
 43. The method of claim 4, wherein theformaldehyde scavenger is 2-Imidazolidone, and wherein the2-Imidazolidone inhibits induction of new cross-links between nucleicacids and polypeptides in the specimen.
 44. The method of claim 1,wherein the protease enzyme is proteinase-K present at a concentrationof from about 4.3 to about 43 U/ml.